The comparative chloroplast genomic analysis of photosynthetic orchids and developing DNA markers to distinguish Phalaenopsis orchids

Jheng, Cheng Fong; Chen, Tien Chih; Lin, Jhong Yi; Chen, Ting Chieh; Wu, Wen Luan; Chang, Chung‐Liang

doi:10.1016/j.plantsci.2012.04.001

Cited by 90 publications

(67 citation statements)

References 40 publications

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“…3). However, 10 common ndh pseudogenes of two Phalaenopsis species showed a high degree of similarities in sequence and indel patterns [33]. Both Erycina and the allied genus Oncidium lost two ndh genes ( ndh F and ndh K) and had six pseudogenes ( ndh B, C, D, G, and J); similar results were obtained from Oncidium and related Oncidiinae varieties [29].…”

Section: Discussionsupporting

confidence: 55%

“…Non-functional chloroplast-encoded ndh genes have been found in CAM and C3 plants [32], including gymnosperms and grasses [68], [73], [74]. Sequence truncations and indels are common phenomena in orchid chloroplast-encoded ndh genes [17], [28]–[33], [75]. Pseudogenization or loss of the ndh gene did not correlate well with the divergent patterns of Epidendroideae lineages observed in the phylogenetic trees (Fig.…”

Section: Discussionmentioning

confidence: 91%

“…Gower Ramsey [33]. Of the examined 30 genes in above-mentioned seven orchids, 15 potential RNA editing sites out of 11 genes ( atp A, atp F, clp P, mat K, pet B, psb F, rpl 20, rpo A, rpo B, rpo C1 and ycf 3) were shared; the number of shared editing sites increased in Epidendroideae species (28 sites out of 16 genes) (Table S5 and [33]). Therefore, RNA editing is more conserved from the same subfamily than which from different subfamily.…”

Section: Discussionmentioning

confidence: 98%

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Comparative Chloroplast Genomes of Photosynthetic Orchids: Insights into Evolution of the Orchidaceae and Development of Molecular Markers for Phylogenetic Applications

et al. 2014

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The orchid family Orchidaceae is one of the largest angiosperm families, including many species of important economic value. While chloroplast genomes are very informative for systematics and species identification, there is very limited information available on chloroplast genomes in the Orchidaceae. Here, we report the complete chloroplast genomes of the medicinal plant Dendrobium officinale and the ornamental orchid Cypripedium macranthos, demonstrating their gene content and order and potential RNA editing sites. The chloroplast genomes of the above two species and five known photosynthetic orchids showed similarities in structure as well as gene order and content, but differences in the organization of the inverted repeat/small single-copy junction and ndh genes. The organization of the inverted repeat/small single-copy junctions in the chloroplast genomes of these orchids was classified into four types; we propose that inverted repeats flanking the small single-copy region underwent expansion or contraction among Orchidaceae. The AT-rich regions of the ycf1 gene in orchids could be linked to the recombination of inverted repeat/small single-copy junctions. Relative species in orchids displayed similar patterns of variation in ndh gene contents. Furthermore, fifteen highly divergent protein-coding genes were identified, which are useful for phylogenetic analyses in orchids. To test the efficiency of these genes serving as markers in phylogenetic analyses, coding regions of four genes (accD, ccsA, matK, and ycf1) were used as a case study to construct phylogenetic trees in the subfamily Epidendroideae. High support was obtained for placement of previously unlocated subtribes Collabiinae and Dendrobiinae in the subfamily Epidendroideae. Our findings expand understanding of the diversity of orchid chloroplast genomes and provide a reference for study of the molecular systematics of this family.

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Section: Discussionsupporting

confidence: 55%

Section: Discussionmentioning

confidence: 91%

Section: Discussionmentioning

confidence: 98%

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Comparative Chloroplast Genomes of Photosynthetic Orchids: Insights into Evolution of the Orchidaceae and Development of Molecular Markers for Phylogenetic Applications

et al. 2014

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“…These complete cp genome sequences have been widely used in developing useful molecular markers (Kung, 1989; Awasthi et al, 2012; Dong et al, 2012; Jheng et al, 2012; Chen and Melis, 2013) and for molecular phylogenetic studies (Cai et al, 2006; Jansen et al, 2006, 2007; Samson et al, 2007; Hirao et al, 2008; Tangphatsornruang et al, 2009; Takano and Okada, 2011; Turner et al, 2013; Gaudeul et al, 2014). Here, we report the first complete genome sequence of M. glyptostroboides (GenBank accession number: KR061358) based on Illumina high-throughput sequencing technology.…”

Section: Introductionmentioning

confidence: 99%

The complete chloroplast genome sequence of the relict woody plant Metasequoia glyptostroboides Hu et Cheng

Chen

Hao

et al. 2015

Front. Plant Sci.

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Metasequoia glyptostroboides Hu et Cheng is the only species in the genus Metasequoia Miki ex Hu et Cheng, which belongs to the Cupressaceae family. There were around 10 species in the Metasequoia genus, which were widely spread across the Northern Hemisphere during the Cretaceous of the Mesozoic and in the Cenozoic. M. glyptostroboides is the only remaining representative of this genus. Here, we report the complete chloroplast (cp) genome sequence and the cp genomic features of M. glyptostroboides. The M. glyptostroboides cp genome is 131,887 bp in length, with a total of 117 genes comprised of 82 protein-coding genes, 31 tRNA genes and four rRNA genes. In this genome, 11 forward repeats, nine palindromic repeats, and 15 tandem repeats were detected. A total of 188 perfect microsatellites were detected through simple sequence repeat (SSR) analysis and these were distributed unevenly within the cp genome. Comparison of the cp genome structure and gene order to those of several other land plants indicated that a copy of the inverted repeat (IR) region, which was found to be IR region A (IRA), was lost in the M. glyptostroboides cp genome. The five most divergent and five most conserved genes were determined and further phylogenetic analysis was performed among plant species, especially for related species in conifers. Finally, phylogenetic analysis demonstrated that M. glyptostroboides is a sister species to Cryptomeria japonica (L. F.) D. Don and to Taiwania cryptomerioides Hayata. The complete cp genome sequence information of M. glyptostroboides will be great helpful for further investigations of this endemic relict woody plant and for in-depth understanding of the evolutionary history of the coniferous cp genomes, especially for the position of M. glyptostroboides in plant systematics and evolution.

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“…These regions are conserved regions of clustered variation called hotspots, containing SNPs and indels [25,26]. The rpoC2, rpoC1, and ycf1 genes are known as hotspots for variation [9,25,26,40]. Therefore, Fritillaria cp genomes contain general hotspot regions for genetic variation as in other land plants.…”

Section: Discussionmentioning

confidence: 99%

The Complete Chloroplast Genome Sequences of Fritillaria ussuriensis Maxim. and Fritillaria cirrhosa D. Don, and Comparative Analysis with Other Fritillaria Species

Park¹,

Kim²,

Yeo³

et al. 2017

Preprint

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Abstract:The genus Fritillaria belongs to the widely distributed family Liliaceae. The bulbs of Fritillaria ussuriensis and Fritillaria cirrhosa are valuable herbaceous medicinal ingredients. However, they are still used indiscriminately in herbal medicine. Identification and molecular phylogenic analysis of Fritillaria species is therefore required. Here, we report the complete chloroplast (cp) genome sequences of F. ussuriensis and F. cirrhosa. The two Fritillaria cp genomes were 151,524 and 151,083 bp in length, respectively, including a pair of inverted repeat regions (52,678 and 52,156 bp) separated by a large single copy region (81,732 and 81,390 bp) and small single copy region (17,114 and 17,537 bp). A total of 111 genes in F. ussuriensis and 112 in F. cirrhosa comprised 77 proteincoding genes in F. ussuriensis and 78 in F. cirrhosa, 30 tRNA genes, and four rRNA genes. The gene order, content, and orientation of the two Fritillaria cp genomes exhibited the general structure of flowering plants, and were similar to those of other Fritillaria species. Comparison of the six Fritillaria species' cp genomes indicated seven highly divergent regions in intergenic spacers and in the matK, rpoC1, rpoC2, ycf1, ycf2, ndhD, and ndhF coding regions. We established the position of the six species through phylogenic analysis. The complete chloroplast genome sequences of two Fritillaria species will be useful genomics resources for identification of Fritillaria species and for studying the phylogenetic relationship among Fritillaria species within the Liliaceae family.

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The comparative chloroplast genomic analysis of photosynthetic orchids and developing DNA markers to distinguish Phalaenopsis orchids

Cited by 90 publications

References 40 publications

Comparative Chloroplast Genomes of Photosynthetic Orchids: Insights into Evolution of the Orchidaceae and Development of Molecular Markers for Phylogenetic Applications

Comparative Chloroplast Genomes of Photosynthetic Orchids: Insights into Evolution of the Orchidaceae and Development of Molecular Markers for Phylogenetic Applications

The complete chloroplast genome sequence of the relict woody plant Metasequoia glyptostroboides Hu et Cheng

The Complete Chloroplast Genome Sequences of<em> Fritillaria ussuriensis</em> Maxim. and <em>Fritillaria cirrhosa</em> D. Don, and Comparative Analysis with Other<em> Fritillaria</em> Species

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